chr8-8738102-C-T

Variant names:

• chr8-8738102-C-T
• rs554241
• ENST00000522213.5:n.625-14368G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000522213.5(ENSG00000254367):​n.625-14368G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,030 control chromosomes in the GnomAD database, including 2,562 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.17 (2562 hom., cov: 32)
• Consequence: ENSG00000254367 ENST00000522213.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240

Genes affected

ENSG00000254367 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254367	ENST00000522213.5	n.625-14368G>A		intron_variant	Intron 3 of 3	2

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25096 AN: 151914 Hom.: 2557 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.0758

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.160

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.165 AC: 25113 AN: 152030 Hom.: 2562 Cov.: 32 AF XY: 0.163 AC XY: 12133 AN XY: 74308

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.160

Alfa AF: 0.121 Hom.: 654

Bravo AF: 0.169

Asia WGS AF: 0.128 AC: 445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.43
DANN	Benign	0.19

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs554241; hg19: chr8-8595612;